Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1121: Mapping the structure and function of the E1 and E2 glycoproteins... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1121
    TitleMapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
    SampleSindbis TE12 E2-N318Q
    SourceSindbis virus / virus / Sindbis strain TE12
    Map datacenter of virus is where z=0
    Methodsingle particle (icosahedral) reconstruction, at 9 A resolution
    AuthorsMukhopadhyay S / Zhang W / Gabler S / Chipman PR / Strauss EG / Strauss JH / Baker TS / Kuhn RJ / Rossmann MG
    CitationStructure, 2006, 14, 63-73

    Structure, 2006, 14, 63-73 StrPapers
    Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
    Suchetana Mukhopadhyay / Wei Zhang / Stefan Gabler / Paul R Chipman / Ellen G Strauss / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann

    DateDeposition: Apr 8, 2005 / Header (metadata) release: Apr 8, 2005 / Map release: Jan 16, 2006 / Last update: Apr 8, 2005

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 75
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 75
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-1z8y
    • Surface level: 100
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-2xfb
    • Surface level: 100
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-3muw
    • Surface level: 100
    • Imaged by UCSF CHIMERA
    • Download
    3D viewer /

    View / / Stereo:
    Center
    Zoom
    Scale
    slabnear <=> far

    fix: /
    Orientation
    Orientation Rotation
    misc. /
    Show/hide
    Supplemental images

    Downloads & links

    -
    Map

    Fileemd_1121.map.gz (map file in CCP4 format, 335025 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    441 pix
    1.78 A/pix
    = 787.18 A
    441 pix
    1.78 A/pix
    = 787.18 A
    441 pix
    1.78 A/pix
    = 787.18 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.78499 A
    Density
    Contour Level:138, 75 (movie #1):
    Minimum - Maximum-297.65 - 402.47
    Average (Standard dev.)7.03224 (65.0912)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions441441441
    Origin-220-220-220
    Limit220220220
    Spacing441441441
    CellA=B=C: 787.18 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.78498866213151.78498866213151.7849886621315
    M x/y/z441441441
    origin x/y/z0.0000.0000.000
    length x/y/z787.180787.180787.180
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-220-220-220
    NX/NY/NZ441441441
    MAP C/R/S213
    start NC/NR/NS-220-220-220
    NC/NR/NS441441441
    D min/max/mean-297.650402.4707.032

    -
    Supplemental data

    -
    Sample components

    -
    Entire Sindbis TE12 E2-N318Q

    EntireName: Sindbis TE12 E2-N318Q
    Details: Sample is a single deglycosylated virus. For mutagenesis and purification, please see Pletnev et al. (2001) Cell. Virus contains 3 proteins (E1, E2, capsid), a lipid bilyer, and a positive-strand RNA genome.
    Number of components: 1

    -
    Component #1: virus, Sindbis virus

    VirusName: Sindbis virus / a.k.a: Sindbis strain TE12 / Class: VIRION / Details: deglycosylated virus / Empty: No / Enveloped: Yes / Isolate: STRAIN
    MassExperimental: 52 MDa
    SpeciesSpecies: Sindbis virus / virus / Sindbis strain TE12
    Source (natural)Host Species: Homo sapiens / human / Host category: INVERTEBRATES
    Shell #1Name of element: glycoprotein / Diameter: 710 A / T number(triangulation number): 4
    Shell #2Name of element: lipid bilayer / Diameter: 480 A / T number(triangulation number): 4
    Shell #3Name of element: capsid / Diameter: 410 A / T number(triangulation number): 4

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 6 mg/ml / Buffer solution: 20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA / pH: 7.4
    Support filmholey carbon 400 mesh copper grid
    Stainingno staining
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: standard methods / Time resolved state: Vitrified immediately after blotting.
    Details: Vitrification instrument: Purdue manufactured, gravity driven device. Vitrification carried out in hood.

    -
    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200T / Date: Jun 21, 2000 / Details: Low dose
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 38000 X (nominal), 39220 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1100 - 2580 nm
    Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
    Model: GATAN LIQUID NITROGEN / Temperature: K ( 87 - 100 K)
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 27 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 1 / Details: optical density range is 0.33-1.35

    -
    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 7085 / Number of class averages: 3
    Details: The particles were selected interactively at the computer terminal.
    Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: model-based common lines / Software: Purdue Suite / CTF correction: CTF correction of each particle. / Resolution: 9 A / Resolution method: FSC 0.5
    Euler angles: Euler angles (theta, phi, omega) are defined as three successive rotations in a right hand coordinate system. First, the viewer is rotated counterclockwise around the z-axis (angle 'phi') and then rotated counterclockwise around the new y-axis (angle 'theta') and rotate clockwise around the new z-axis (angle 'omega').
    Details: resolution determined by splitting data set into two groups.

    -
    Atomic model buiding

    Modeling #1Software: EMFIT / Refinement protocol: rigid body / Target criteria: sumf / Refinement space: REAL
    Details: Protocol: Rigid body. each protein in the asymmetric unit was fitting individually.
    Input PDB model: 1I9W
    Modeling #2Software: EMFIT / Refinement protocol: rigid body / Target criteria: sumf / Refinement space: REAL
    Details: Protocol: Rigid body. each protein in the asymmetric unit was fitting individually.
    Input PDB model: 1XYK
    Output model

    +
    About Yorodumi

    -
    News

    -
    Sep 15, 2016. EM Navigator & Yorodumi renewed

    EM Navigator & Yorodumi renewed

    • New versions of EM Navigator and Yorodumi started

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    -
    Aug 31, 2016. New EM Navigator & Yorodumi

    New EM Navigator & Yorodumi

    • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
    • Current version will continue as 'legacy version' for some time.

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    +
    Apr 13, 2016. Omokage search got faster

    Omokage search got faster

    • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
    • Enjoy "shape similarity" of biomolecules, more!

    Related info.: Omokage search

    +
    Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

    Read more

    -
    Yorodumi

    Thousand views of thousand structures

    • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
    • All the functionalities will be ported from the levgacy version.
    • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

    Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

    Read more